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- PDB-8q8q: Cryo-EM structure of the magnesium channel CtMrs2 in the open state -

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Basic information

Entry
Database: PDB / ID: 8q8q
TitleCryo-EM structure of the magnesium channel CtMrs2 in the open state
ComponentsMagnesium channel Mrs2
KeywordsMEMBRANE PROTEIN / Magnesium channel Mrs2
Function / homologyChem-LOP
Function and homology information
Biological speciesThermochaetoides thermophila (fungus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.22 Å
AuthorsGourdon, P. / Li, P.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Swedish Research Council Sweden
Citation
Journal: Nat Struct Mol Biol / Year: 2025
Title: Closed and open structures of the eukaryotic magnesium channel Mrs2 reveal the auto-ligand-gating regulation mechanism.
Authors: Ping Li / Shiyan Liu / Johan Wallerstein / Rhiza Lyne E Villones / Peng Huang / Karin Lindkvist-Petersson / Gabriele Meloni / Kefeng Lu / Kristine Steen Jensen / Sara I Liin / Pontus Gourdon /
Abstract: The CorA/Mrs2 family of pentameric proteins are cardinal for the influx of Mg across cellular membranes, importing the cation to mitochondria in eukaryotes. Yet, the conducting and regulation ...The CorA/Mrs2 family of pentameric proteins are cardinal for the influx of Mg across cellular membranes, importing the cation to mitochondria in eukaryotes. Yet, the conducting and regulation mechanisms of permeation remain elusive, particularly for the eukaryotic Mrs2 members. Here, we report closed and open Mrs2 cryo-electron microscopy structures, accompanied by functional characterization. Mg flux is permitted by a narrow pore, gated by methionine and arginine residues in the closed state. Transition between the conformations is orchestrated by two pairs of conserved sensor-serving Mg-binding sites in the mitochondrial matrix lumen, located in between monomers. At lower levels of Mg, these ions are stripped, permitting an alternative, symmetrical shape, maintained by the RDLR motif that replaces one of the sensor site pairs in the open conformation. Thus, our findings collectively establish the molecular basis for selective Mg influx of Mrs2 and an auto-ligand-gating regulation mechanism.
#1: Journal: Acta Crystallogr D Struct Biol / Year: 2018
Title: Real-space refinement in PHENIX for cryo-EM and crystallography.
Authors: Pavel V Afonine / Billy K Poon / Randy J Read / Oleg V Sobolev / Thomas C Terwilliger / Alexandre Urzhumtsev / Paul D Adams /
Abstract: This article describes the implementation of real-space refinement in the phenix.real_space_refine program from the PHENIX suite. The use of a simplified refinement target function enables very fast ...This article describes the implementation of real-space refinement in the phenix.real_space_refine program from the PHENIX suite. The use of a simplified refinement target function enables very fast calculation, which in turn makes it possible to identify optimal data-restraint weights as part of routine refinements with little runtime cost. Refinement of atomic models against low-resolution data benefits from the inclusion of as much additional information as is available. In addition to standard restraints on covalent geometry, phenix.real_space_refine makes use of extra information such as secondary-structure and rotamer-specific restraints, as well as restraints or constraints on internal molecular symmetry. The re-refinement of 385 cryo-EM-derived models available in the Protein Data Bank at resolutions of 6 Å or better shows significant improvement of the models and of the fit of these models to the target maps.
History
DepositionAug 18, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 27, 2024Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2024Group: Data collection / Database references / Category: citation / citation_author / em_admin
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Revision 1.2Dec 11, 2024Group: Data collection / Database references / Category: citation / citation_author / em_admin
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Revision 1.3Dec 25, 2024Group: Data collection / Database references / Category: citation_author / em_admin
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Revision 1.4Mar 26, 2025Group: Data collection / Database references / Category: citation / em_admin
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Magnesium channel Mrs2
B: Magnesium channel Mrs2
C: Magnesium channel Mrs2
D: Magnesium channel Mrs2
E: Magnesium channel Mrs2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)248,83413
Polymers245,4515
Non-polymers3,3828
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "E" and resid 162 through 501)
d_2ens_1chain "B"
d_3ens_1chain "C"
d_4ens_1chain "D"
d_5ens_1chain "A"

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ALAALAVALVALAA162 - 48356 - 377
d_12LOPLOPLOPLOPAF601
d_21ALAALAVALVALBB162 - 48356 - 377
d_22LOPLOPLOPLOPBJ601
d_31ALAALAVALVALCC162 - 48356 - 377
d_32LOPLOPLOPLOPCK601
d_41ALAALAVALVALDD162 - 48356 - 377
d_42LOPLOPLOPLOPDL601
d_51ALAALAVALVALEE162 - 48356 - 377
d_52LOPLOPLOPLOPEM601

NCS oper:
IDCodeMatrixVector
1given(-0.808719136229, -0.588194985044, 0.000135154119857), (0.588194995132, -0.80871913865, 4.98307956079E-5), (7.99914993188E-5, 0.000119796094853, 0.999999989625)410.633373008, 209.103065707, -0.0292807635654
2given(-0.809782437036, 0.586730063745, 0.000486791571987), (-0.586730029189, -0.80978257685, 0.000226004306007), (0.000526798854423, -0.000102600915542, 0.999999855978)209.433074771, 410.540586905, -0.0753025132526
3given(0.309034357215, 0.951050864552, 0.000138184163272), (-0.951050874567, 0.309034354984, 3.7755495879E-5), (-6.79625676834E-6, -0.000143087914731, 0.99999998974)-44.5800026231, 281.307305784, 0.0292945003736
4given(0.309372193279, -0.950941006064, -0.000221385968231), (0.950940945729, 0.309372255954, -0.000353528130933), (0.00040467507293, -0.000101153208748, 0.999999913003)281.262609864, -44.5329239314, -0.0326585761182

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Components

#1: Protein
Magnesium channel Mrs2


Mass: 49090.285 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermochaetoides thermophila (fungus) / Production host: Saccharomyces cerevisiae (brewer's yeast)
#2: Chemical
ChemComp-LOP / (1R)-2-{[(R)-(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(DODECANOYLOXY)METHYL]ETHYL (9Z)-OCTADEC-9-ENOATE / LAURYL OLEYL PHOSPHATIDYL ETHANOLAMINE


Mass: 661.890 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C35H68NO8P / Comment: phospholipid*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Mrs2 homo-pentamer / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Thermochaetoides thermophila (fungus)
Source (recombinant)Organism: Saccharomyces cerevisiae (brewer's yeast)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 600 nm
Image recordingElectron dose: 49.958 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.22 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 116609 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 57.3 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002512880
ELECTRON MICROSCOPYf_angle_d0.475917355
ELECTRON MICROSCOPYf_chiral_restr0.03742045
ELECTRON MICROSCOPYf_plane_restr0.00382185
ELECTRON MICROSCOPYf_dihedral_angle_d6.69151860
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2BELECTRON MICROSCOPYNCS constraints1.30406208675E-10
ens_1d_3CELECTRON MICROSCOPYNCS constraints7.92945487113E-13
ens_1d_4DELECTRON MICROSCOPYNCS constraints6.11136990983E-11
ens_1d_5EELECTRON MICROSCOPYNCS constraints2.16118432251E-13

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